perf: Eliminate double serialization, add SQLite tuning, optimize hot paths

11 isomorphic performance fixes from deep audit (no behavior changes):

- Eliminate double serialization: store_payload now accepts pre-serialized
  bytes (&[u8]) instead of re-serializing from serde_json::Value. Uses
  Cow<[u8]> for zero-copy when compression is disabled.
- Add SQLite cache_size (64MB) and mmap_size (256MB) pragmas
- Replace SELECT-then-INSERT label upserts with INSERT...ON CONFLICT
  RETURNING in both issues.rs and merge_requests.rs
- Replace INSERT + SELECT milestone upsert with RETURNING
- Use prepare_cached for 5 hot-path queries in extractor.rs
- Optimize compute_list_hash: index-sort + incremental SHA-256 instead
  of clone+sort+join+hash
- Pre-allocate embedding float-to-bytes buffer with Vec::with_capacity
- Replace RandomState::new() in rand_jitter with atomic counter XOR nanos
- Remove redundant per-note payload storage (discussion payload contains
  all notes already)
- Change transform_issue to accept &GitLabIssue (avoids full struct clone)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

src/embedding/pipeline.rs

@@ -329,7 +329,10 @@ fn store_embedding(
 ) -> Result<()> {
     let rowid = encode_rowid(doc_id, chunk_index as i64);
 
-    let embedding_bytes: Vec<u8> = embedding.iter().flat_map(|f| f.to_le_bytes()).collect();
+    let mut embedding_bytes = Vec::with_capacity(embedding.len() * 4);
+    for f in embedding {
+        embedding_bytes.extend_from_slice(&f.to_le_bytes());
+    }
 
     conn.execute(
         "INSERT OR REPLACE INTO embeddings (rowid, embedding) VALUES (?1, ?2)",